Atomistry » Sodium » PDB 5kd8-5kw9 » 5kqn
Atomistry »
  Sodium »
    PDB 5kd8-5kw9 »
      5kqn »

Sodium in PDB 5kqn: Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei

Enzymatic activity of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqn was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.18 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.986, 114.174, 175.544, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.2

Other elements in 5kqn:

The structure of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kqn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kqn

Go back to Sodium Binding Sites List in 5kqn
Sodium binding site 1 out of 2 in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.6
occ:1.00
O A:GLY122 2.3 19.4 1.0
O A:GLY124 2.3 20.2 1.0
O A:HOH960 2.3 25.9 1.0
O A:SER494 2.3 22.3 1.0
O A:HOH995 2.5 22.9 1.0
C A:SER494 3.2 21.6 1.0
C A:GLY124 3.5 18.4 1.0
C A:GLY122 3.5 19.1 1.0
CA A:ARG123 3.5 18.3 1.0
C A:ARG123 3.5 17.9 1.0
N A:GLY124 3.6 19.3 1.0
O A:HOH1421 4.0 25.3 1.0
CA A:SER494 4.0 20.6 1.0
N A:ARG123 4.0 19.3 1.0
OD2 A:ASP427 4.0 23.5 1.0
N A:ASP495 4.1 18.0 1.0
O A:ARG123 4.1 19.8 1.0
CA A:GLY124 4.1 18.9 1.0
O A:HOH1023 4.1 30.4 1.0
CB A:ASP427 4.2 24.0 1.0
CB A:SER494 4.2 22.2 1.0
CA A:ASP495 4.4 19.6 1.0
N A:GLY125 4.6 17.3 1.0
CB A:ASP495 4.6 21.4 1.0
CD1 A:TYR117 4.6 20.7 1.0
CG A:ASP427 4.7 22.2 1.0
OE1 A:GLU198 4.7 28.2 1.0
CA A:GLY122 4.7 20.7 1.0
OE2 A:GLU198 4.7 40.8 1.0
CE1 A:TYR117 4.8 22.0 1.0
CA A:GLY125 4.8 17.2 1.0
CB A:ARG123 4.8 21.5 1.0
OE2 A:GLU128 4.9 40.1 1.0

Sodium binding site 2 out of 2 in 5kqn

Go back to Sodium Binding Sites List in 5kqn
Sodium binding site 2 out of 2 in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:21.5
occ:1.00
O B:HOH994 2.2 24.5 1.0
O B:SER494 2.4 23.1 1.0
O B:GLY124 2.4 20.9 1.0
O B:HOH963 2.4 25.3 1.0
O B:GLY122 2.4 20.2 1.0
C B:SER494 3.2 23.3 1.0
C B:GLY124 3.5 21.2 1.0
C B:GLY122 3.5 18.5 1.0
C B:ARG123 3.6 19.5 1.0
N B:GLY124 3.6 19.4 1.0
CA B:ARG123 3.6 18.8 1.0
CA B:SER494 4.0 21.4 1.0
O B:HOH1341 4.0 22.1 1.0
O B:HOH990 4.0 37.4 1.0
N B:ARG123 4.1 19.4 1.0
OD2 B:ASP427 4.1 24.9 1.0
N B:ASP495 4.1 18.8 1.0
CB B:ASP427 4.1 22.2 1.0
CA B:GLY124 4.2 21.8 1.0
CB B:SER494 4.2 20.4 1.0
O B:ARG123 4.2 19.2 1.0
CA B:ASP495 4.4 21.1 1.0
CB B:ASP495 4.5 21.4 1.0
N B:GLY125 4.6 19.0 1.0
CD1 B:TYR117 4.6 21.7 1.0
OE2 B:GLU198 4.7 41.7 1.0
CG B:ASP427 4.7 23.6 1.0
OE1 B:GLU198 4.8 27.4 1.0
CA B:GLY122 4.8 20.5 1.0
CE1 B:TYR117 4.8 20.9 1.0
OE2 B:GLU128 4.9 41.9 1.0
CA B:GLY125 4.9 20.6 1.0
CB B:ARG123 4.9 21.7 1.0
OG B:SER494 5.0 21.9 1.0
O B:HOH1181 5.0 35.1 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Mon Oct 7 22:09:36 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy